Download biochemistry

Microbial Chemistry
Dr.Mohammad Shakeeb,MD
Specialist in clinical
pathology/microbiology and
immunology
INTRODUCTION
• chemistry is an important component of a
microbiology.
• A microbe can be thought of as a “bag” of
chemicals that interact with each other in
various ways.
• The various ways microorganisms function
and survive in their environment depend on
their chemical makeup.
INTRODUCTION
• Even the most simple procaryotic cells consist
of very large molecules (macromolecules).
 Deoxyribonucleic acid (DNA).
 Ribonucleic acid (RNA).
 Proteins.
 Lipids.
 Polysaccharides.
INTRODUCTION
• These macromolecules can be broken down
into smaller units or “building blocks”.
 monosaccharides (simple sugars).
 fatty acids.
 amino acids.
 nucleotides.
• The macromolecules and building blocks
found in cells are collectively referred to as
biological molecules.
INTRODUCTION
• building blocks can be broken down into even
smaller molecules such as water, carbon
dioxide, ammonia, sulfides, and phosphates,
which in turn can be broken down into atoms
of carbon (C), hydrogen (H), oxygen
(O),nitrogen (N), sulfur (S), phosphorus (P).
INTRODUCTION
• Organic chemistry is the study of compounds
that contain carbon.
• inorganic chemistry involves all other
chemical reactions.
• biochemistry is the chemistry of living cells.
ORGANIC CHEMISTRY
ORGANIC CHEMISTRY
• Organic compounds are compounds that
contain carbon.
• organic chemistry is that branch of the science
of chemistry that specializes in the study of
organic compounds.
• Although some organic compounds are
associated with living organisms, many are
not.
ORGANIC CHEMISTRY
Carbon Bonds
• Carbon atoms have a valence of four.
• carbon atom can bond to four other atoms.
ORGANIC CHEMISTRY
Carbon Bonds
• The uniqueness of carbon lies in the ability of
its atoms to bond to each other to form a
multitude of compounds.
• There are three ways in which carbon atoms
can bond to each other:
ORGANIC CHEMISTRY
Carbon Bonds
• When atoms of other elements attach to
available bonds of carbon atoms, compounds
are formed.
• if only hydrogen atoms are bonded to the
available
bonds,
compounds
called
hydrocarbons are formed.
ORGANIC CHEMISTRY
Carbon Bonds
• When more than two carbons are linked
together, longer molecules are formed.
ORGANIC CHEMISTRY
Carbon Bonds
• A series of many carbon atoms bonded
together is referred to as a chain.
• Long-chain carbon compounds are usually
liquids or solids, whereas short-chain carbon
compounds are gases.
ORGANIC CHEMISTRY
Cyclic Compounds
• Carbon atoms may link to carbon atoms to
close the chain, forming rings or cyclic
compounds.
• An example is benzene, which has six carbons
and six hydrogens.
• some compounds contain fused rings (e.g.,
double- or triple-ringed compounds).
ORGANIC CHEMISTRY
BIOCHEMISTRY
BIOCHEMISTRY
• Biochemistry is the study of biology at the
molecular level and can, thus, be thought of as
the chemistry of life or the chemistry of living
organisms.
• Biomolecules are usually large molecules
(called
macromolecules)
and
include
carbohydrates, lipids, proteins, and nucleic
acids.
BIOCHEMISTRY
• Microorganisms also absorb their essential
nutrients into the cell by various means.
• These nutrients are then used in metabolic
reactions as sources of energy and as building
blocks
for
enzymes,
structural
macromolecules, and genetic materials.
BIOCHEMISTRY
• Carbohydrates
• Carbohydrates are biomolecules composed of
carbon, hydrogen, and oxygen, in the ratio of 1:2:1,
or simply CH2O.
 Monosaccharides
• The simplest carbohydrates are sugars, and the
smallest sugars.
• The most important monosaccharide in nature is
glucose (C6H12O6).
BIOCHEMISTRY
BIOCHEMISTRY
• Monosaccharides may contain from three to nine
carbon atoms.
BIOCHEMISTRY
Disaccharides
• Disaccharides (di meaning “two”) are double-ringed
sugars that result from the combination of two
monosaccharides.
• synthesis
of
a
disaccharide
from
two
monosaccharides by removal of a water molecule is
called a dehydration synthesis reaction.
• The bond holding the two monosaccharides together
is called a glycosidic bond; it is a type of covalent
bond.
BIOCHEMISTRY
BIOCHEMISTRY
• Sucrose, lactose, and maltose are examples of
disaccharides.
• Disaccharides react with water in a process called a
hydrolysis reaction, which causes them to break
down into two monosaccharides:
BIOCHEMISTRY
• Peptidoglycan is a complex macromolecular
network found in the cell walls of all members of
Bacteria.
• Peptidoglycan consists of a repeating disaccharide,
attached by polypeptides (proteins) to form a lattice
that surrounds and protects the entire bacterial cell.
• Several antibiotics (including penicillin) prevent the
final cross-linking of the rows of disaccharides, thus
weakening the cell wall and leading to lysis
(bursting) of the bacterial cell.
BIOCHEMISTRY
• Polysaccharides
• Polysaccharides can be defined as carbohydrates that
contain many monosaccharides.
• Polysaccharides, such as glycogen, starch, and
cellulose, are examples of polymers—molecules
consisting of many similar subunits. In the case of
polysaccharides, the repeating subunits are
monosaccharides.
BIOCHEMISTRY
• Many bacteria produce polysaccharide
capsules, which protect the bacteria from
being phagocytized (eaten) by white blood
cells.
• algal cells have cellulose cell walls to provide
support and shape as well as protection
against the environment.
BIOCHEMISTRY
• When polysaccharides combine with other chemical
groups (amines, lipids, and amino acids), extremely
complex macromolecules are formed that serve
specific purposes.
• Glucosamine and galactosamine (amine derivatives
of glucose and galactose, respectively) are important
constituents of the supporting polysaccharides in
connective tissue fibers, cartilage, and chitin.
BIOCHEMISTRY
• Chitin is the main component of the hard outer
covering of insects, spiders, and crabs, and is also
found in the cell walls of fungi.
• The main portion of the rigid cell wall of bacteria
consists of amino sugars and short polypeptide
chains that combine to form the peptidoglycan
layer.
BIOCHEMISTRY
Lipids
• Lipids are essential constituents of almost all living cells.
• lipids can be classified into the following categories:
 • Waxes
 • Fats and oils
 • Phospholipids
 • Glycolipids
 • Steroids
 • Prostaglandins and leukotrienes
BIOCHEMISTRY
Fatty Acids
• the building blocks of lipids.
• Fatty acids are long-chain carboxylic acids that are
insoluble in water.
• Saturated fatty acids contain only single bonds
between the carbon atoms.
• Monounsaturated fatty acids have one double bond
in the carbon chain.
• Polyunsaturated fatty acids contain two or more
double bonds.
BIOCHEMISTRY
Waxes
• A wax consists of a saturated fatty acid and a longchain alcohol.
• The waxes that are present in the cell walls of
Mycobacterium tuberculosis (the causative agent of
tuberculosis) are responsible for several interesting
characteristics of this bacterium.
• M. tuberculosis cell be phagocytized by a phagocytic
white blood cell (a phagocyte), the waxes protect the
cell from being digested.
BIOCHEMISTRY
• the waxes in the cell walls of M. tuberculosis make
the organism difficult to stain.
• In the acid-fast staining procedure, for example, it is
necessary to heat the carbolfuchsin dye to drive it
into the cell.
• once the cell has been stained, the waxes prevent
decolorization of the cell when a mixture of acid and
alcohol is applied.
• Because the cell does not decolorize in the presence
of acid, the organism is described as being acid-fast.
BIOCHEMISTRY
Fats and Oils
• Fats and oils are also known as triglycerides, because
they are composed of glycerol (a three-carbon
alcohol) and three fatty acids.
BIOCHEMISTRY
Phospholipids
• Phospholipids contain glycerol, fatty acids, a
phosphate group, and an alcohol.
• There are two types: glycerophospholipids (also
called phosphoglycerides) and sphingolipids.
BIOCHEMISTRY
• In addition to phospholipids, the outer membrane of
Gram-negative bacterial cell walls contains lipoproteins
and lipopolysaccharide (LPS).
• LPS consists of a lipid portion and a polysaccharide
portion.
• The lipid portion is called lipid-A or endotoxin.
• When endotoxin is present in the human. bloodstream, it
can cause very serious physiologic conditions (e.g., fever
and septic shock).
• The cell walls of Gram-positive bacteria do not contain
LPS.
BIOCHEMISTRY
Proteins
• All proteins are polymers of amino acids.
• Some proteins are the structural components of
membranes, cells, and tissues.
• others are enzymes and hormones that chemically
control the metabolic balance within both the cell
and the entire organism.
• they vary widely in the number of amino acids
present and in the sequence of amino acids as well
as their size, configuration, and functions.
BIOCHEMISTRY
• Proteins contain carbon, hydrogen, oxygen, nitrogen,
and sometimes sulfur.
 Amino Acid Structure
• A total of 23 different amino acids have been found in
proteins, 20 primary or naturally occurring amino acids plus 3
secondary amino acids.
• Each amino acid is composed of carbon, hydrogen, oxygen,
and nitrogen.
• 3 of the amino acids also have sulfur atoms in the molecule.
BIOCHEMISTRY
BIOCHEMISTRY
BIOCHEMISTRY
 Protein Structure
• When water is removed, by dehydration synthesis,
amino acids become linked together by a covalent
bond, referred to as a peptide bond.
BIOCHEMISTRY
Enzymes
• Enzymes are protein molecules produced by living
cells as “instructed” by genes on the chromosomes.
• Enzymes are referred to as biological catalysts—
biologic molecules that catalyze metabolic reactions.
• catalyst is defined as an agent that speeds up a
chemical reaction without being consumed in the
process.
BIOCHEMISTRY
Nucleic Acids
• DNA is the “hereditary molecule”—the molecule that
contains the genes and genetic code.
• DNA makes up the major portion of chromosomes.
• The information in DNA must flow to the rest of the
cell for the cell to function properly.
• this flow of information is accomplished by RNA
molecules.
• RNA molecules participate in the conversion of the
genetic code into proteins and other gene products.
BIOCHEMISTRY
Structure
• The building blocks of nucleic acid polymers are
called nucleotides.
• Nucleotides consist of three subunits: a nitrogencontaining (nitrogenous) base, a five-carbon sugar
(pentose), and a phosphate group, joined together.
• The building blocks of DNA are called DNA
nucleotides, whereas the building blocks of RNA are
called RNA nucleotides.
BIOCHEMISTRY
BIOCHEMISTRY
BIOCHEMISTRY
• three types of RNA, which are named for the
function they serve: messenger RNA (mRNA),
ribosomal RNA (rRNA), and transfer RNA (tRNA).
BIOCHEMISTRY
BIOCHEMISTRY
BIOCHEMISTRY
• The bonding forces of the double stranded polymer
cause it to assume the shape of a double-helix,
which is similar to a right-handed spiral staircase.
BIOCHEMISTRY
 DNA Replication
• It occurs by separation of the DNA strands and the
building of complementary strands by the addition of the
correct DNA nucleotides.
• The most important enzyme required for DNA replication
is DNA polymerase.
• Other enzymes are also required, including DNA helicase
and DNA topoisomerase (which initiate the separation of
the two strands of the DNA molecule), primase (which
synthesizes a short RNA primer), and DNA ligase (which
connects fragments of newly synthesized DNA).
BIOCHEMISTRY
• The duplicated DNA of the chromosomes can then
be separated during cell division.
• so that each daughter cell contains the same number
of chromosomes, the same genes, and the same
amount of DNA as in the parent cell.
BIOCHEMISTRY
Gene Expression
• It was Francis Crick who, in 1957, proposed what is
referred to as the Central Dogma to explain the flow
of genetic information within a cell.
• DNA → mRNA → protein
• The Central Dogma (also known as the “one gene–
one protein hypothesis”) states that:
1. The genetic information contained in one gene of a DNA
molecule is used to make one molecule of mRNA by a
process known as transcription.
BIOCHEMISTRY
2. The genetic information in that mRNA molecule is then used
to make one protein by a process known as translation.
• The primary enzyme involved in transcription is
called RNA polymerase (DNA-dependent RNA
polymerase).
BIOCHEMISTRY
• The process by which the genetic information within
an mRNA molecule is used to make a specific protein
is called translation.
• Translation occurs at a ribosome.